I'm thinking if you want to parallel characters to the events of the books then I'd see Dean as Jace, Jo as Clary, Anna as Simon, Cas as Alec, Balthazar as Magnus, Ruby as Isabelle... Maybe Sam as Sebastian/Johnathan. So that leaves a lot of pairings open for you to play with.

Or you could just do some story in the same universe if you're cool with some Annaby, you could do something with Anna as a Shadowhunter getting into a fight with demon Ruby that gets a little out of hand and kind of flirty. idk.

I'd pretty much be happy with anything